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authorDana Robinson <derobins@hdfgroup.org>2016-11-29 20:06:37 (GMT)
committerDana Robinson <derobins@hdfgroup.org>2016-11-29 20:06:37 (GMT)
commitd3dbe9d90ee71b231b3264e1d62d3efbae3242ef (patch)
treeb8d706ac89af0822c0ac5cf0e1ab78fa5c3b5b1e /src
parent8fd8115715a2890da432cf2708109a35ea1c33e5 (diff)
parent3d2beeec1fb63c8c2bac4658df382ea7a9d61e05 (diff)
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Merge branch 'develop' into eoc_valgrind_bugfix
Diffstat (limited to 'src')
-rw-r--r--src/H5B2.c4
-rw-r--r--src/H5B2int.c2
-rw-r--r--src/H5B2pkg.h4
-rw-r--r--src/H5Dchunk.c1
-rw-r--r--src/H5EA.c199
-rw-r--r--src/H5EAcache.c19
-rw-r--r--src/H5F.c97
-rw-r--r--src/H5FA.c210
-rw-r--r--src/H5FAhdr.c2
-rw-r--r--src/H5FDcore.c43
-rw-r--r--src/H5FDfamily.c47
-rw-r--r--src/H5FDlog.c50
-rw-r--r--src/H5FDsec2.c34
-rw-r--r--src/H5FDstdio.c49
-rw-r--r--src/H5Fint.c103
-rw-r--r--src/H5Zscaleoffset.c52
16 files changed, 549 insertions, 367 deletions
diff --git a/src/H5B2.c b/src/H5B2.c
index bce6a9f..af5fae7 100644
--- a/src/H5B2.c
+++ b/src/H5B2.c
@@ -343,11 +343,11 @@ H5B2_update(H5B2_t *bt2, hid_t dxpl_id, void *udata, H5B2_modify_t op, void *op_
/* Attempt to insert record into B-tree */
if(hdr->depth > 0) {
if(H5B2__update_internal(hdr, dxpl_id, hdr->depth, NULL, &hdr->root, &status, H5B2_POS_ROOT, udata, op, op_data) < 0)
- HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to update record in B-tree internal node")
+ HGOTO_ERROR(H5E_BTREE, H5E_CANTUPDATE, FAIL, "unable to update record in B-tree internal node")
} /* end if */
else {
if(H5B2__update_leaf(hdr, dxpl_id, &hdr->root, &status, H5B2_POS_ROOT, udata, op, op_data) < 0)
- HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to update record in B-tree leaf node")
+ HGOTO_ERROR(H5E_BTREE, H5E_CANTUPDATE, FAIL, "unable to update record in B-tree leaf node")
} /* end else */
/* Sanity check */
diff --git a/src/H5B2int.c b/src/H5B2int.c
index 3bd788c..a8fa59f 100644
--- a/src/H5B2int.c
+++ b/src/H5B2int.c
@@ -1925,7 +1925,7 @@ H5B2__update_leaf(H5B2_hdr_t *hdr, hid_t dxpl_id, H5B2_node_ptr_t *curr_node_ptr
if((hdr->cls->store)(H5B2_LEAF_NREC(leaf, hdr, idx), udata) < 0)
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, FAIL, "unable to insert record into leaf node")
- /* Mark the node as dirty if it changed */
+ /* Mark the node as dirty */
leaf_flags |= H5AC__DIRTIED_FLAG;
/* Indicate that the record was inserted */
diff --git a/src/H5B2pkg.h b/src/H5B2pkg.h
index edac296..6a385d4 100644
--- a/src/H5B2pkg.h
+++ b/src/H5B2pkg.h
@@ -261,8 +261,8 @@ typedef struct H5B2_leaf_cache_ud_t {
#ifdef H5B2_TESTING
/* Node information for testing */
typedef struct H5B2_node_info_test_t {
- unsigned depth; /* Depth of node */
- unsigned nrec; /* Number of records in node */
+ uint16_t depth; /* Depth of node */
+ uint16_t nrec; /* Number of records in node */
} H5B2_node_info_test_t;
#endif /* H5B2_TESTING */
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index dde83fe..7637339 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -4851,7 +4851,6 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim)
* will never change. */
chk_store.chunk.scaled = scaled;
H5D_BUILD_IO_INFO_RD(&chk_io_info, dset, dxpl_cache, dxpl_id, H5AC_rawdata_dxpl_id, &chk_store, NULL);
- chk_io_info.raw_dxpl_id = H5AC_rawdata_dxpl_id;
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
diff --git a/src/H5EA.c b/src/H5EA.c
index 8a4c5a1..9c3f3e7 100644
--- a/src/H5EA.c
+++ b/src/H5EA.c
@@ -78,6 +78,8 @@ static herr_t
H5EA__lookup_elmt(const H5EA_t *ea, hid_t dxpl_id, hsize_t idx, hbool_t will_extend,
unsigned thing_acc, void **thing, uint8_t **thing_elmt_buf,
hsize_t *thing_elmt_idx, H5EA__unprotect_func_t *thing_unprot_func);
+static H5EA_t *H5EA__new(H5F_t *f, hid_t dxpl_id, haddr_t ea_addr,
+ hbool_t from_open, void *ctx_udata);
/*********************/
@@ -116,49 +118,45 @@ H5FL_BLK_DEFINE(ea_native_elmt);
/*-------------------------------------------------------------------------
- * Function: H5EA_create
+ * Function: H5EA__new
*
- * Purpose: Creates a new empty extensible array in the file.
+ * Purpose: Allocate and initialize a new extensible array wrapper in memory
*
- * Return: Pointer to earray wrapper on success
+ * Return: Pointer to earray wrapper success
* NULL on failure
*
* Programmer: Quincey Koziol
- * koziol@hdfgroup.org
- * Jun 17 2008
+ * koziol@lbl.gov
+ * Oct 10 2016
*
*-------------------------------------------------------------------------
*/
-BEGIN_FUNC(PRIV, ERR,
+BEGIN_FUNC(STATIC, ERR,
H5EA_t *, NULL, NULL,
-H5EA_create(H5F_t *f, hid_t dxpl_id, const H5EA_create_t *cparam, void *ctx_udata))
+H5EA__new(H5F_t *f, hid_t dxpl_id, haddr_t ea_addr, hbool_t from_open, void *ctx_udata))
/* Local variables */
H5EA_t *ea = NULL; /* Pointer to new extensible array */
H5EA_hdr_t *hdr = NULL; /* The extensible array header information */
- haddr_t ea_addr; /* Array header address */
/*
* Check arguments.
*/
HDassert(f);
- HDassert(cparam);
-
- /* H5EA interface sanity check */
- HDcompile_assert(H5EA_NUM_CLS_ID == NELMTS(H5EA_client_class_g));
-
- /* Create extensible array header */
- if(HADDR_UNDEF == (ea_addr = H5EA__hdr_create(f, dxpl_id, cparam, ctx_udata)))
- H5E_THROW(H5E_CANTINIT, "can't create extensible array header")
+ HDassert(H5F_addr_defined(ea_addr));
/* Allocate extensible array wrapper */
- if(NULL == (ea = H5FL_MALLOC(H5EA_t)))
+ if(NULL == (ea = H5FL_CALLOC(H5EA_t)))
H5E_THROW(H5E_CANTALLOC, "memory allocation failed for extensible array info")
/* Lock the array header into memory */
- if(NULL == (hdr = H5EA__hdr_protect(f, dxpl_id, ea_addr, ctx_udata, H5AC__NO_FLAGS_SET)))
+ if(NULL == (hdr = H5EA__hdr_protect(f, dxpl_id, ea_addr, ctx_udata, H5AC__READ_ONLY_FLAG)))
H5E_THROW(H5E_CANTPROTECT, "unable to load extensible array header")
+ /* Check for pending array deletion */
+ if(from_open && hdr->pending_delete)
+ H5E_THROW(H5E_CANTOPENOBJ, "can't open extensible array pending deletion")
+
/* Point extensible array wrapper at header and bump it's ref count */
ea->hdr = hdr;
if(H5EA__hdr_incr(ea->hdr) < 0)
@@ -182,6 +180,57 @@ CATCH
if(ea && H5EA_close(ea, dxpl_id) < 0)
H5E_THROW(H5E_CLOSEERROR, "unable to close extensible array")
+END_FUNC(STATIC) /* end H5EA__new() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5EA_create
+ *
+ * Purpose: Creates a new empty extensible array in the file.
+ *
+ * Return: Pointer to earray wrapper on success
+ * NULL on failure
+ *
+ * Programmer: Quincey Koziol
+ * koziol@hdfgroup.org
+ * Jun 17 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PRIV, ERR,
+H5EA_t *, NULL, NULL,
+H5EA_create(H5F_t *f, hid_t dxpl_id, const H5EA_create_t *cparam, void *ctx_udata))
+
+ /* Local variables */
+ H5EA_t *ea = NULL; /* Pointer to new extensible array */
+ haddr_t ea_addr; /* Array header address */
+
+ /*
+ * Check arguments.
+ */
+ HDassert(f);
+ HDassert(cparam);
+
+ /* H5EA interface sanity check */
+ HDcompile_assert(H5EA_NUM_CLS_ID == NELMTS(H5EA_client_class_g));
+
+ /* Create extensible array header */
+ if(HADDR_UNDEF == (ea_addr = H5EA__hdr_create(f, dxpl_id, cparam, ctx_udata)))
+ H5E_THROW(H5E_CANTINIT, "can't create extensible array header")
+
+ /* Allocate and initialize new extensible array wrapper */
+ if(NULL == (ea = H5EA__new(f, dxpl_id, ea_addr, FALSE, ctx_udata)))
+ H5E_THROW(H5E_CANTINIT, "allocation and/or initialization failed for extensible array wrapper")
+
+ /* Set the return value */
+ ret_value = ea;
+
+CATCH
+
+ if(!ret_value)
+ if(ea && H5EA_close(ea, dxpl_id) < 0)
+ H5E_THROW(H5E_CLOSEERROR, "unable to close extensible array")
+
END_FUNC(PRIV) /* end H5EA_create() */
@@ -205,7 +254,6 @@ H5EA_open(H5F_t *f, hid_t dxpl_id, haddr_t ea_addr, void *ctx_udata))
/* Local variables */
H5EA_t *ea = NULL; /* Pointer to new extensible array wrapper */
- H5EA_hdr_t *hdr = NULL; /* The extensible array header information */
/*
* Check arguments.
@@ -213,37 +261,15 @@ H5EA_open(H5F_t *f, hid_t dxpl_id, haddr_t ea_addr, void *ctx_udata))
HDassert(f);
HDassert(H5F_addr_defined(ea_addr));
- /* Load the array header into memory */
- if(NULL == (hdr = H5EA__hdr_protect(f, dxpl_id, ea_addr, ctx_udata, H5AC__READ_ONLY_FLAG)))
- H5E_THROW(H5E_CANTPROTECT, "unable to load extensible array header, address = %llu", (unsigned long long)ea_addr)
-
- /* Check for pending array deletion */
- if(hdr->pending_delete)
- H5E_THROW(H5E_CANTOPENOBJ, "can't open extensible array pending deletion")
-
- /* Create fractal heap info */
- if(NULL == (ea = H5FL_MALLOC(H5EA_t)))
- H5E_THROW(H5E_CANTALLOC, "memory allocation failed for extensible array info")
-
- /* Point extensible array wrapper at header */
- ea->hdr = hdr;
- if(H5EA__hdr_incr(ea->hdr) < 0)
- H5E_THROW(H5E_CANTINC, "can't increment reference count on shared array header")
-
- /* Increment # of files using this array header */
- if(H5EA__hdr_fuse_incr(ea->hdr) < 0)
- H5E_THROW(H5E_CANTINC, "can't increment file reference count on shared array header")
-
- /* Set file pointer for this array open context */
- ea->f = f;
+ /* Allocate and initialize new extensible array wrapper */
+ if(NULL == (ea = H5EA__new(f, dxpl_id, ea_addr, TRUE, ctx_udata)))
+ H5E_THROW(H5E_CANTINIT, "allocation and/or initialization failed for extensible array wrapper")
/* Set the return value */
ret_value = ea;
CATCH
- if(hdr && H5EA__hdr_unprotect(hdr, dxpl_id, H5AC__NO_FLAGS_SET) < 0)
- H5E_THROW(H5E_CANTUNPROTECT, "unable to release extensible array header")
if(!ret_value)
if(ea && H5EA_close(ea, dxpl_id) < 0)
H5E_THROW(H5E_CLOSEERROR, "unable to close extensible array")
@@ -818,26 +844,28 @@ H5EA_close(H5EA_t *ea, hid_t dxpl_id))
*/
HDassert(ea);
- /* Decrement file reference & check if this is the last open extensible array using the shared array header */
- if(0 == H5EA__hdr_fuse_decr(ea->hdr)) {
- /* Set the shared array header's file context for this operation */
- ea->hdr->f = ea->f;
-
- /* Shut down anything that can't be put in the header's 'flush' callback */
-
- /* Check for pending array deletion */
- if(ea->hdr->pending_delete) {
- /* Set local info, so array deletion can occur after decrementing the
- * header's ref count
- */
- pending_delete = TRUE;
- ea_addr = ea->hdr->addr;
+ /* Close the header, if it was set */
+ if(ea->hdr) {
+ /* Decrement file reference & check if this is the last open extensible array using the shared array header */
+ if(0 == H5EA__hdr_fuse_decr(ea->hdr)) {
+ /* Set the shared array header's file context for this operation */
+ ea->hdr->f = ea->f;
+
+ /* Shut down anything that can't be put in the header's 'flush' callback */
+
+ /* Check for pending array deletion */
+ if(ea->hdr->pending_delete) {
+ /* Set local info, so array deletion can occur after decrementing the
+ * header's ref count
+ */
+ pending_delete = TRUE;
+ ea_addr = ea->hdr->addr;
+ } /* end if */
} /* end if */
- } /* end if */
- /* Check for pending array deletion */
- if(pending_delete) {
- H5EA_hdr_t *hdr; /* Another pointer to extensible array header */
+ /* Check for pending array deletion */
+ if(pending_delete) {
+ H5EA_hdr_t *hdr; /* Another pointer to extensible array header */
#ifndef NDEBUG
{
@@ -854,33 +882,34 @@ H5EA_close(H5EA_t *ea, hid_t dxpl_id))
}
#endif /* NDEBUG */
- /* Lock the array header into memory */
- /* (OK to pass in NULL for callback context, since we know the header must be in the cache) */
- if(NULL == (hdr = H5EA__hdr_protect(ea->f, dxpl_id, ea_addr, NULL, H5AC__NO_FLAGS_SET)))
- H5E_THROW(H5E_CANTLOAD, "unable to load extensible array header")
+ /* Lock the array header into memory */
+ /* (OK to pass in NULL for callback context, since we know the header must be in the cache) */
+ if(NULL == (hdr = H5EA__hdr_protect(ea->f, dxpl_id, ea_addr, NULL, H5AC__NO_FLAGS_SET)))
+ H5E_THROW(H5E_CANTLOAD, "unable to load extensible array header")
- /* Set the shared array header's file context for this operation */
- hdr->f = ea->f;
+ /* Set the shared array header's file context for this operation */
+ hdr->f = ea->f;
- /* Decrement the reference count on the array header */
- /* (don't put in H5EA_hdr_fuse_decr() as the array header may be evicted
- * immediately -QAK)
- */
- if(H5EA__hdr_decr(ea->hdr) < 0)
- H5E_THROW(H5E_CANTDEC, "can't decrement reference count on shared array header")
+ /* Decrement the reference count on the array header */
+ /* (don't put in H5EA_hdr_fuse_decr() as the array header may be evicted
+ * immediately -QAK)
+ */
+ if(H5EA__hdr_decr(ea->hdr) < 0)
+ H5E_THROW(H5E_CANTDEC, "can't decrement reference count on shared array header")
- /* Delete array, starting with header (unprotects header) */
- if(H5EA__hdr_delete(hdr, dxpl_id) < 0)
- H5E_THROW(H5E_CANTDELETE, "unable to delete extensible array")
+ /* Delete array, starting with header (unprotects header) */
+ if(H5EA__hdr_delete(hdr, dxpl_id) < 0)
+ H5E_THROW(H5E_CANTDELETE, "unable to delete extensible array")
+ } /* end if */
+ else {
+ /* Decrement the reference count on the array header */
+ /* (don't put in H5EA_hdr_fuse_decr() as the array header may be evicted
+ * immediately -QAK)
+ */
+ if(H5EA__hdr_decr(ea->hdr) < 0)
+ H5E_THROW(H5E_CANTDEC, "can't decrement reference count on shared array header")
+ } /* end else */
} /* end if */
- else {
- /* Decrement the reference count on the array header */
- /* (don't put in H5EA_hdr_fuse_decr() as the array header may be evicted
- * immediately -QAK)
- */
- if(H5EA__hdr_decr(ea->hdr) < 0)
- H5E_THROW(H5E_CANTDEC, "can't decrement reference count on shared array header")
- } /* end else */
/* Release the extensible array wrapper */
ea = (H5EA_t *)H5FL_FREE(H5EA_t, ea);
diff --git a/src/H5EAcache.c b/src/H5EAcache.c
index 4210b07..b7846e9 100644
--- a/src/H5EAcache.c
+++ b/src/H5EAcache.c
@@ -893,7 +893,11 @@ H5EA__cache_iblock_notify(H5AC_notify_action_t action, void *_thing))
break;
default:
+#ifdef NDEBUG
H5E_THROW(H5E_BADVALUE, "unknown action from metadata cache")
+#else /* NDEBUG */
+ HDassert(0 && "Unknown action?!?");
+#endif /* NDEBUG */
} /* end switch */
CATCH
@@ -955,7 +959,6 @@ H5EA__cache_sblock_get_initial_load_size(void *_udata, size_t *image_len))
/* Check arguments */
HDassert(udata);
HDassert(udata->hdr);
- HDassert(udata->parent);
HDassert(udata->sblk_idx > 0);
HDassert(H5F_addr_defined(udata->sblk_addr));
HDassert(image_len);
@@ -1293,7 +1296,11 @@ H5EA__cache_sblock_notify(H5AC_notify_action_t action, void *_thing))
break;
default:
+#ifdef NDEBUG
H5E_THROW(H5E_BADVALUE, "unknown action from metadata cache")
+#else /* NDEBUG */
+ HDassert(0 && "Unknown action?!?");
+#endif /* NDEBUG */
} /* end switch */
CATCH
@@ -1355,7 +1362,6 @@ H5EA__cache_dblock_get_initial_load_size(void *_udata, size_t *image_len))
/* Check arguments */
HDassert(udata);
HDassert(udata->hdr);
- HDassert(udata->parent);
HDassert(udata->nelmts > 0);
HDassert(image_len);
@@ -1694,7 +1700,11 @@ H5EA__cache_dblock_notify(H5AC_notify_action_t action, void *_thing))
break;
default:
+#ifdef NDEBUG
H5E_THROW(H5E_BADVALUE, "unknown action from metadata cache")
+#else /* NDEBUG */
+ HDassert(0 && "Unknown action?!?");
+#endif /* NDEBUG */
} /* end switch */
CATCH
@@ -1802,7 +1812,6 @@ H5EA__cache_dblk_page_get_initial_load_size(void *_udata, size_t *image_len))
/* Check arguments */
HDassert(udata);
HDassert(udata->hdr);
- HDassert(udata->parent);
HDassert(image_len);
/* Set the image length size */
@@ -2063,7 +2072,11 @@ H5EA__cache_dblk_page_notify(H5AC_notify_action_t action, void *_thing))
break;
default:
+#ifdef NDEBUG
H5E_THROW(H5E_BADVALUE, "unknown action from metadata cache")
+#else /* NDEBUG */
+ HDassert(0 && "Unknown action?!?");
+#endif /* NDEBUG */
} /* end switch */
CATCH
diff --git a/src/H5F.c b/src/H5F.c
index f663036..6b087ce 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -1367,6 +1367,103 @@ done:
/*-------------------------------------------------------------------------
+ * Function: H5Fget_metadata_read_retry_info
+ *
+ * Purpose: To retrieve the collection of read retries for metadata items with checksum.
+ *
+ * Return: Success: non-negative on success
+ * Failure: Negative
+ *
+ * Programmer: Vailin Choi; October 2013
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info)
+{
+ H5F_t *file; /* File object for file ID */
+ unsigned i, j; /* Local index variable */
+ size_t tot_size; /* Size of each retries[i] */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_API(FAIL)
+ H5TRACE2("e", "i*x", file_id, info);
+
+ /* Check args */
+ if(!info)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no info struct")
+
+ /* Get the file pointer */
+ if(NULL == (file = (H5F_t *)H5I_object_verify(file_id, H5I_FILE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "not a file ID")
+
+ /* Copy the # of bins for "retries" array */
+ info->nbins = file->shared->retries_nbins;
+
+ /* Initialize the array of "retries" */
+ HDmemset(info->retries, 0, sizeof(info->retries));
+
+ /* Return if there are no bins -- no retries */
+ if(!info->nbins)
+ HGOTO_DONE(SUCCEED);
+
+ /* Calculate size for each retries[i] */
+ tot_size = info->nbins * sizeof(uint32_t);
+
+ /* Map and copy information to info's retries for metadata items with tracking for read retries */
+ j = 0;
+ for(i = 0; i < H5AC_NTYPES; i++) {
+ switch(i) {
+ case H5AC_OHDR_ID:
+ case H5AC_OHDR_CHK_ID:
+ case H5AC_BT2_HDR_ID:
+ case H5AC_BT2_INT_ID:
+ case H5AC_BT2_LEAF_ID:
+ case H5AC_FHEAP_HDR_ID:
+ case H5AC_FHEAP_DBLOCK_ID:
+ case H5AC_FHEAP_IBLOCK_ID:
+ case H5AC_FSPACE_HDR_ID:
+ case H5AC_FSPACE_SINFO_ID:
+ case H5AC_SOHM_TABLE_ID:
+ case H5AC_SOHM_LIST_ID:
+ case H5AC_EARRAY_HDR_ID:
+ case H5AC_EARRAY_IBLOCK_ID:
+ case H5AC_EARRAY_SBLOCK_ID:
+ case H5AC_EARRAY_DBLOCK_ID:
+ case H5AC_EARRAY_DBLK_PAGE_ID:
+ case H5AC_FARRAY_HDR_ID:
+ case H5AC_FARRAY_DBLOCK_ID:
+ case H5AC_FARRAY_DBLK_PAGE_ID:
+ case H5AC_SUPERBLOCK_ID:
+ HDassert(j < H5F_NUM_METADATA_READ_RETRY_TYPES);
+ if(file->shared->retries[i] != NULL) {
+ /* Allocate memory for retries[i]
+ *
+ * This memory should be released by the user with
+ * the H5free_memory() call.
+ */
+ if(NULL == (info->retries[j] = (uint32_t *)H5MM_malloc(tot_size)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
+
+ /* Copy the information */
+ HDmemcpy(info->retries[j], file->shared->retries[i], tot_size);
+ } /* end if */
+
+ /* Increment location in info->retries[] array */
+ j++;
+ break;
+
+ default:
+ break;
+ } /* end switch */
+ } /* end for */
+
+done:
+ FUNC_LEAVE_API(ret_value)
+} /* end H5Fget_metadata_read_retry_info() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5Fget_free_sections
*
* Purpose: To get free-space section information for free-space manager with
diff --git a/src/H5FA.c b/src/H5FA.c
index 4435af0..c6c2e1b 100644
--- a/src/H5FA.c
+++ b/src/H5FA.c
@@ -64,6 +64,8 @@
/********************/
/* Local Prototypes */
/********************/
+static H5FA_t *H5FA__new(H5F_t *f, hid_t dxpl_id, haddr_t fa_addr,
+ hbool_t from_open, void *ctx_udata);
/*********************/
@@ -103,51 +105,44 @@ H5FL_BLK_DEFINE(fa_native_elmt);
/*-------------------------------------------------------------------------
- * Function: H5FA_create
+ * Function: H5FA__new
*
- * Purpose: Creates a new fixed array (header) in the file.
+ * Purpose: Allocate and initialize a new fixe array wrapper in memory
*
- * Return: Pointer to fixed array wrapper on success
+ * Return: Pointer to farray wrapper success
* NULL on failure
*
- * Programmer: Vailin Choi
- * Thursday, April 30, 2009
+ * Programmer: Quincey Koziol
+ * koziol@lbl.gov
+ * Oct 17 2016
*
*-------------------------------------------------------------------------
*/
-BEGIN_FUNC(PRIV, ERR,
+BEGIN_FUNC(STATIC, ERR,
H5FA_t *, NULL, NULL,
-H5FA_create(H5F_t *f, hid_t dxpl_id, const H5FA_create_t *cparam, void *ctx_udata))
+H5FA__new(H5F_t *f, hid_t dxpl_id, haddr_t fa_addr, hbool_t from_open, void *ctx_udata))
/* Local variables */
H5FA_t *fa = NULL; /* Pointer to new fixed array */
H5FA_hdr_t *hdr = NULL; /* The fixed array header information */
- haddr_t fa_addr; /* Fixed Array header address */
-
-#ifdef H5FA_DEBUG
-HDfprintf(stderr, "%s: Called\n", FUNC);
-#endif /* H5FA_DEBUG */
/*
* Check arguments.
*/
HDassert(f);
- HDassert(cparam);
-
- /* H5FA interface sanity check */
- HDcompile_assert(H5FA_NUM_CLS_ID == NELMTS(H5FA_client_class_g));
-
- /* Create fixed array header */
- if(HADDR_UNDEF == (fa_addr = H5FA__hdr_create(f, dxpl_id, cparam, ctx_udata)))
- H5E_THROW(H5E_CANTINIT, "can't create fixed array header")
+ HDassert(H5F_addr_defined(fa_addr));
/* Allocate fixed array wrapper */
- if(NULL == (fa = H5FL_MALLOC(H5FA_t)))
- H5E_THROW(H5E_CANTALLOC, "memory allocation failed for fixed array info")
+ if(NULL == (fa = H5FL_CALLOC(H5FA_t)))
+ H5E_THROW(H5E_CANTALLOC, "memory allocation failed for fixed array info")
/* Lock the array header into memory */
- if(NULL == (hdr = H5FA__hdr_protect(f, dxpl_id, fa_addr, ctx_udata, H5AC__NO_FLAGS_SET)))
- H5E_THROW(H5E_CANTPROTECT, "unable to load fixed array header")
+ if(NULL == (hdr = H5FA__hdr_protect(f, dxpl_id, fa_addr, ctx_udata, H5AC__READ_ONLY_FLAG)))
+ H5E_THROW(H5E_CANTPROTECT, "unable to load fixed array header")
+
+ /* Check for pending array deletion */
+ if(from_open && hdr->pending_delete)
+ H5E_THROW(H5E_CANTOPENOBJ, "can't open fixed array pending deletion")
/* Point fixed array wrapper at header and bump it's ref count */
fa->hdr = hdr;
@@ -172,6 +167,56 @@ CATCH
if(fa && H5FA_close(fa, dxpl_id) < 0)
H5E_THROW(H5E_CLOSEERROR, "unable to close fixed array")
+END_FUNC(STATIC) /* end H5FA__new() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5FA_create
+ *
+ * Purpose: Creates a new fixed array (header) in the file.
+ *
+ * Return: Pointer to fixed array wrapper on success
+ * NULL on failure
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PRIV, ERR,
+H5FA_t *, NULL, NULL,
+H5FA_create(H5F_t *f, hid_t dxpl_id, const H5FA_create_t *cparam, void *ctx_udata))
+
+ /* Local variables */
+ H5FA_t *fa = NULL; /* Pointer to new fixed array */
+ haddr_t fa_addr; /* Fixed array header address */
+
+ /*
+ * Check arguments.
+ */
+ HDassert(f);
+ HDassert(cparam);
+
+ /* H5FA interface sanity check */
+ HDcompile_assert(H5FA_NUM_CLS_ID == NELMTS(H5FA_client_class_g));
+
+ /* Create fixed array header */
+ if(HADDR_UNDEF == (fa_addr = H5FA__hdr_create(f, dxpl_id, cparam, ctx_udata)))
+ H5E_THROW(H5E_CANTINIT, "can't create fixed array header")
+
+ /* Allocate and initialize new fixed array wrapper */
+ if(NULL == (fa = H5FA__new(f, dxpl_id, fa_addr, FALSE, ctx_udata)))
+ H5E_THROW(H5E_CANTINIT, "allocation and/or initialization failed for fixed array wrapper")
+
+ /* Set the return value */
+ ret_value = fa;
+
+CATCH
+
+ if(!ret_value)
+ if(fa && H5FA_close(fa, dxpl_id) < 0)
+ H5E_THROW(H5E_CLOSEERROR, "unable to close fixed array")
+
END_FUNC(PRIV) /* end H5FA_create() */
@@ -194,7 +239,6 @@ H5FA_open(H5F_t *f, hid_t dxpl_id, haddr_t fa_addr, void *ctx_udata))
/* Local variables */
H5FA_t *fa = NULL; /* Pointer to new fixed array wrapper */
- H5FA_hdr_t *hdr = NULL; /* The fixed array header information */
/*
* Check arguments.
@@ -202,40 +246,15 @@ H5FA_open(H5F_t *f, hid_t dxpl_id, haddr_t fa_addr, void *ctx_udata))
HDassert(f);
HDassert(H5F_addr_defined(fa_addr));
- /* Load the array header into memory */
-#ifdef H5FA_DEBUG
-HDfprintf(stderr, "%s: fa_addr = %a\n", FUNC, fa_addr);
-#endif /* H5FA_DEBUG */
- if(NULL == (hdr = H5FA__hdr_protect(f, dxpl_id, fa_addr, ctx_udata, H5AC__READ_ONLY_FLAG)))
- H5E_THROW(H5E_CANTPROTECT, "unable to load fixed array header, address = %llu", (unsigned long long)fa_addr)
-
- /* Check for pending array deletion */
- if(hdr->pending_delete)
- H5E_THROW(H5E_CANTOPENOBJ, "can't open fixed array pending deletion")
-
- /* Create fixed array info */
- if(NULL == (fa = H5FL_MALLOC(H5FA_t)))
- H5E_THROW(H5E_CANTALLOC, "memory allocation failed for fixed array info")
-
- /* Point fixed array wrapper at header */
- fa->hdr = hdr;
- if(H5FA__hdr_incr(fa->hdr) < 0)
- H5E_THROW(H5E_CANTINC, "can't increment reference count on shared array header")
-
- /* Increment # of files using this array header */
- if(H5FA__hdr_fuse_incr(fa->hdr) < 0)
- H5E_THROW(H5E_CANTINC, "can't increment file reference count on shared array header")
-
- /* Set file pointer for this array open context */
- fa->f = f;
+ /* Allocate and initialize new fixed array wrapper */
+ if(NULL == (fa = H5FA__new(f, dxpl_id, fa_addr, TRUE, ctx_udata)))
+ H5E_THROW(H5E_CANTINIT, "allocation and/or initialization failed for fixed array wrapper")
/* Set the return value */
ret_value = fa;
CATCH
- if(hdr && H5FA__hdr_unprotect(hdr, dxpl_id, H5AC__NO_FLAGS_SET) < 0)
- H5E_THROW(H5E_CANTUNPROTECT, "unable to release fixed array header")
if(!ret_value)
if(fa && H5FA_close(fa, dxpl_id) < 0)
H5E_THROW(H5E_CLOSEERROR, "unable to close fixed array")
@@ -534,26 +553,28 @@ H5FA_close(H5FA_t *fa, hid_t dxpl_id))
*/
HDassert(fa);
- /* Decrement file reference & check if this is the last open fixed array using the shared array header */
- if(0 == H5FA__hdr_fuse_decr(fa->hdr)) {
- /* Set the shared array header's file context for this operation */
- fa->hdr->f = fa->f;
-
- /* Shut down anything that can't be put in the header's 'flush' callback */
-
- /* Check for pending array deletion */
- if(fa->hdr->pending_delete) {
- /* Set local info, so array deletion can occur after decrementing the
- * header's ref count
- */
- pending_delete = TRUE;
- fa_addr = fa->hdr->addr;
+ /* Close the header, if it was set */
+ if(fa->hdr) {
+ /* Decrement file reference & check if this is the last open fixed array using the shared array header */
+ if(0 == H5FA__hdr_fuse_decr(fa->hdr)) {
+ /* Set the shared array header's file context for this operation */
+ fa->hdr->f = fa->f;
+
+ /* Shut down anything that can't be put in the header's 'flush' callback */
+
+ /* Check for pending array deletion */
+ if(fa->hdr->pending_delete) {
+ /* Set local info, so array deletion can occur after decrementing the
+ * header's ref count
+ */
+ pending_delete = TRUE;
+ fa_addr = fa->hdr->addr;
+ } /* end if */
} /* end if */
- } /* end if */
- /* Check for pending array deletion */
- if(pending_delete) {
- H5FA_hdr_t *hdr; /* Another pointer to fixed array header */
+ /* Check for pending array deletion */
+ if(pending_delete) {
+ H5FA_hdr_t *hdr; /* Another pointer to fixed array header */
#ifndef NDEBUG
{
@@ -570,33 +591,34 @@ H5FA_close(H5FA_t *fa, hid_t dxpl_id))
}
#endif /* NDEBUG */
- /* Lock the array header into memory */
- /* (OK to pass in NULL for callback context, since we know the header must be in the cache) */
- if(NULL == (hdr = H5FA__hdr_protect(fa->f, dxpl_id, fa_addr, NULL, H5AC__NO_FLAGS_SET)))
- H5E_THROW(H5E_CANTLOAD, "unable to load fixed array header")
+ /* Lock the array header into memory */
+ /* (OK to pass in NULL for callback context, since we know the header must be in the cache) */
+ if(NULL == (hdr = H5FA__hdr_protect(fa->f, dxpl_id, fa_addr, NULL, H5AC__NO_FLAGS_SET)))
+ H5E_THROW(H5E_CANTLOAD, "unable to load fixed array header")
- /* Set the shared array header's file context for this operation */
- hdr->f = fa->f;
+ /* Set the shared array header's file context for this operation */
+ hdr->f = fa->f;
- /* Decrement the reference count on the array header */
- /* (don't put in H5FA_hdr_fuse_decr() as the array header may be evicted
- * immediately -QAK)
- */
- if(H5FA__hdr_decr(fa->hdr) < 0)
- H5E_THROW(H5E_CANTDEC, "can't decrement reference count on shared array header")
+ /* Decrement the reference count on the array header */
+ /* (don't put in H5FA_hdr_fuse_decr() as the array header may be evicted
+ * immediately -QAK)
+ */
+ if(H5FA__hdr_decr(fa->hdr) < 0)
+ H5E_THROW(H5E_CANTDEC, "can't decrement reference count on shared array header")
- /* Delete array, starting with header (unprotects header) */
- if(H5FA__hdr_delete(hdr, dxpl_id) < 0)
- H5E_THROW(H5E_CANTDELETE, "unable to delete fixed array")
+ /* Delete array, starting with header (unprotects header) */
+ if(H5FA__hdr_delete(hdr, dxpl_id) < 0)
+ H5E_THROW(H5E_CANTDELETE, "unable to delete fixed array")
+ } /* end if */
+ else {
+ /* Decrement the reference count on the array header */
+ /* (don't put in H5FA_hdr_fuse_decr() as the array header may be evicted
+ * immediately -QAK)
+ */
+ if(H5FA__hdr_decr(fa->hdr) < 0)
+ H5E_THROW(H5E_CANTDEC, "can't decrement reference count on shared array header")
+ } /* end else */
} /* end if */
- else {
- /* Decrement the reference count on the array header */
- /* (don't put in H5FA_hdr_fuse_decr() as the array header may be evicted
- * immediately -QAK)
- */
- if(H5FA__hdr_decr(fa->hdr) < 0)
- H5E_THROW(H5E_CANTDEC, "can't decrement reference count on shared array header")
- } /* end else */
/* Release the fixed array wrapper */
fa = H5FL_FREE(H5FA_t, fa);
diff --git a/src/H5FAhdr.c b/src/H5FAhdr.c
index d844f06..d6e32dc 100644
--- a/src/H5FAhdr.c
+++ b/src/H5FAhdr.c
@@ -119,6 +119,7 @@ H5FA__hdr_alloc(H5F_t *f))
ret_value = hdr;
CATCH
+
if(!ret_value)
if(hdr && H5FA__hdr_dest(hdr) < 0)
H5E_THROW(H5E_CANTFREE, "unable to destroy fixed array header")
@@ -225,6 +226,7 @@ H5FA__hdr_create(H5F_t *f, hid_t dxpl_id, const H5FA_create_t *cparam,
ret_value = hdr->addr;
CATCH
+
if(!H5F_addr_defined(ret_value))
if(hdr) {
/* Release header's disk space */
diff --git a/src/H5FDcore.c b/src/H5FDcore.c
index f29e231..9090679 100644
--- a/src/H5FDcore.c
+++ b/src/H5FDcore.c
@@ -1479,23 +1479,31 @@ done:
static herr_t
H5FD_core_lock(H5FD_t *_file, hbool_t rw)
{
- H5FD_core_t *file = (H5FD_core_t*)_file; /* VFD file struct */
- int lock; /* The type of lock */
- herr_t ret_value = SUCCEED; /* Return value */
+ H5FD_core_t *file = (H5FD_core_t*)_file; /* VFD file struct */
+ int lock_flags; /* file locking flags */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
HDassert(file);
+
+ /* Only set the lock if there is a file descriptor. If no file
+ * descriptor, this is a no-op.
+ */
if(file->fd >= 0) {
- /* Determine the type of lock */
- lock = rw ? LOCK_EX : LOCK_SH;
-
- /* Place the lock with non-blocking */
- if(HDflock(file->fd, lock | LOCK_NB) < 0)
- HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to flock file")
- }
- /* Otherwise a noop */
+ /* Set exclusive or shared lock based on rw status */
+ lock_flags = rw ? LOCK_EX : LOCK_SH;
+
+ /* Place a non-blocking lock on the file */
+ if(HDflock(file->fd, lock_flags | LOCK_NB) < 0) {
+ if(ENOSYS == errno)
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "file locking disabled on this file system (use HDF5_USE_FILE_LOCKING environment variable to override)")
+ else
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to lock file")
+ } /* end if */
+
+ } /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -1525,11 +1533,16 @@ H5FD_core_unlock(H5FD_t *_file)
if(file->fd >= 0) {
- if(HDflock(file->fd, LOCK_UN) < 0)
- HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to flock (unlock) file")
- }
- /* Otherwise a noop */
+ if(HDflock(file->fd, LOCK_UN) < 0) {
+ if(ENOSYS == errno)
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "file locking disabled on this file system (use HDF5_USE_FILE_LOCKING environment variable to override)")
+ else
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to unlock file")
+ } /* end if */
+
+ } /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_core_unlock() */
+
diff --git a/src/H5FDfamily.c b/src/H5FDfamily.c
index 7ec8751..f0d4dba 100644
--- a/src/H5FDfamily.c
+++ b/src/H5FDfamily.c
@@ -1339,33 +1339,37 @@ done:
static herr_t
H5FD_family_lock(H5FD_t *_file, hbool_t rw)
{
- H5FD_family_t *file = (H5FD_family_t *)_file; /* VFD file struct */
- unsigned u, i; /* Local index variable */
- herr_t ret_value = SUCCEED; /* Return value */
+ H5FD_family_t *file = (H5FD_family_t *)_file; /* VFD file struct */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
/* Place the lock on all the member files */
- for(u = 0; u < file->nmembs; u++) {
- if(file->memb[u]) {
+ for(u = 0; u < file->nmembs; u++)
+ if(file->memb[u])
if(H5FD_lock(file->memb[u], rw) < 0)
- break;
- } /* end if */
- } /* end for */
+ break;
- if(u < file->nmembs) { /* Try to unlock the member files done before */
- for(i = 0; i < u; i++) {
- if(H5FD_unlock(file->memb[i]) < 0)
- /* Push error, but keep going*/
- HDONE_ERROR(H5E_IO, H5E_CANTUNLOCK, FAIL, "unable to unlock member files")
- }
- HGOTO_ERROR(H5E_IO, H5E_CANTLOCK, FAIL, "unable to lock member files")
+ /* If one of the locks failed, try to unlock the locked member files
+ * in an attempt to return to a fully unlocked state.
+ */
+ if(u < file->nmembs) {
+ unsigned v; /* Local index variable */
+
+ for(v = 0; v < v; v++) {
+ if(H5FD_unlock(file->memb[v]) < 0)
+ /* Push error, but keep going */
+ HDONE_ERROR(H5E_IO, H5E_CANTUNLOCK, FAIL, "unable to unlock member files")
+ } /* end for */
+ HGOTO_ERROR(H5E_IO, H5E_CANTLOCK, FAIL, "unable to lock member files")
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_family_lock() */
+
/*-------------------------------------------------------------------------
* Function: H5FD_family_unlock
*
@@ -1381,19 +1385,18 @@ static herr_t
H5FD_family_unlock(H5FD_t *_file)
{
H5FD_family_t *file = (H5FD_family_t *)_file; /* VFD file struct */
- unsigned u; /* Local index variable */
- herr_t ret_value = SUCCEED; /* Return value */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
/* Remove the lock on the member files */
- for(u = 0; u < file->nmembs; u++) {
- if(file->memb[u]) {
+ for(u = 0; u < file->nmembs; u++)
+ if(file->memb[u])
if(H5FD_unlock(file->memb[u]) < 0)
- HGOTO_ERROR(H5E_IO, H5E_CANTUNLOCK, FAIL, "unable to unlock member files")
- } /* end if */
- } /* end for */
+ HGOTO_ERROR(H5E_IO, H5E_CANTUNLOCK, FAIL, "unable to unlock member files")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5FD_family_unlock() */
+
diff --git a/src/H5FDlog.c b/src/H5FDlog.c
index 9f5dfa5..a2891cb 100644
--- a/src/H5FDlog.c
+++ b/src/H5FDlog.c
@@ -1567,15 +1567,7 @@ static herr_t
H5FD_log_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_UNUSED closing)
{
H5FD_log_t *file = (H5FD_log_t *)_file;
-#ifdef H5_HAVE_WIN32_API
- LARGE_INTEGER li; /* 64-bit (union) integer for SetFilePointer() call */
- DWORD dwPtrLow; /* Low-order pointer bits from SetFilePointer()
- * Only used as an error code here.
- */
- DWORD dwError; /* DWORD error code from GetLastError() */
- BOOL bError; /* Boolean error flag */
-#endif /* H5_HAVE_WIN32_API */
-herr_t ret_value = SUCCEED; /* Return value */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@@ -1586,6 +1578,14 @@ herr_t ret_value = SUCCEED; /* Return value */
#ifdef H5_HAVE_GETTIMEOFDAY
struct timeval timeval_start, timeval_stop;
#endif /* H5_HAVE_GETTIMEOFDAY */
+#ifdef H5_HAVE_WIN32_API
+ LARGE_INTEGER li; /* 64-bit (union) integer for SetFilePointer() call */
+ DWORD dwPtrLow; /* Low-order pointer bits from SetFilePointer()
+ * Only used as an error code here.
+ */
+ DWORD dwError; /* DWORD error code from GetLastError() */
+ BOOL bError; /* Boolean error flag */
+#endif /* H5_HAVE_WIN32_API */
#ifdef H5_HAVE_GETTIMEOFDAY
if(file->fa.flags & H5FD_LOG_TIME_TRUNCATE)
@@ -1677,21 +1677,25 @@ done:
static herr_t
H5FD_log_lock(H5FD_t *_file, hbool_t rw)
{
- H5FD_log_t *file = (H5FD_log_t *)_file;
- int lock;
- herr_t ret_value = SUCCEED; /* Return value */
+ H5FD_log_t *file = (H5FD_log_t *)_file; /* VFD file struct */
+ int lock_flags; /* file locking flags */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
/* Sanity check */
HDassert(file);
- /* Determine the type of lock */
- lock = rw ? LOCK_EX : LOCK_SH;
+ /* Set exclusive or shared lock based on rw status */
+ lock_flags = rw ? LOCK_EX : LOCK_SH;
- /* Place the lock with non-blocking */
- if(HDflock(file->fd, lock | LOCK_NB) < 0)
- HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to flock file")
+ /* Place a non-blocking lock on the file */
+ if(HDflock(file->fd, lock_flags | LOCK_NB) < 0) {
+ if(ENOSYS == errno)
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "file locking disabled on this file system (use HDF5_USE_FILE_LOCKING environment variable to override)")
+ else
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to lock file")
+ } /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -1712,15 +1716,19 @@ done:
static herr_t
H5FD_log_unlock(H5FD_t *_file)
{
- H5FD_log_t *file = (H5FD_log_t *)_file; /* VFD file struct */
- herr_t ret_value = SUCCEED; /* Return value */
+ H5FD_log_t *file = (H5FD_log_t *)_file; /* VFD file struct */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
HDassert(file);
- if(HDflock(file->fd, LOCK_UN) < 0)
- HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to flock (unlock) file")
+ if(HDflock(file->fd, LOCK_UN) < 0) {
+ if(ENOSYS == errno)
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "file locking disabled on this file system (use HDF5_USE_FILE_LOCKING environment variable to override)")
+ else
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to unlock file")
+ } /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c
index bb8f004..04a0790 100644
--- a/src/H5FDsec2.c
+++ b/src/H5FDsec2.c
@@ -922,20 +922,24 @@ done:
static herr_t
H5FD_sec2_lock(H5FD_t *_file, hbool_t rw)
{
- H5FD_sec2_t *file = (H5FD_sec2_t *)_file; /* VFD file struct */
- int lock; /* The type of lock */
- herr_t ret_value = SUCCEED; /* Return value */
+ H5FD_sec2_t *file = (H5FD_sec2_t *)_file; /* VFD file struct */
+ int lock_flags; /* file locking flags */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
HDassert(file);
- /* Determine the type of lock */
- lock = rw ? LOCK_EX : LOCK_SH;
-
- /* Place the lock with non-blocking */
- if(HDflock(file->fd, lock | LOCK_NB) < 0)
- HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to flock file")
+ /* Set exclusive or shared lock based on rw status */
+ lock_flags = rw ? LOCK_EX : LOCK_SH;
+
+ /* Place a non-blocking lock on the file */
+ if(HDflock(file->fd, lock_flags | LOCK_NB) < 0) {
+ if(ENOSYS == errno)
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "file locking disabled on this file system (use HDF5_USE_FILE_LOCKING environment variable to override)")
+ else
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to lock file")
+ } /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -956,15 +960,19 @@ done:
static herr_t
H5FD_sec2_unlock(H5FD_t *_file)
{
- H5FD_sec2_t *file = (H5FD_sec2_t *)_file; /* VFD file struct */
- herr_t ret_value = SUCCEED; /* Return value */
+ H5FD_sec2_t *file = (H5FD_sec2_t *)_file; /* VFD file struct */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
HDassert(file);
- if(HDflock(file->fd, LOCK_UN) < 0)
- HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to flock (unlock) file")
+ if(HDflock(file->fd, LOCK_UN) < 0) {
+ if(ENOSYS == errno)
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "file locking disabled on this file system (use HDF5_USE_FILE_LOCKING environment variable to override)")
+ else
+ HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, FAIL, "unable to unlock file")
+ } /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5FDstdio.c b/src/H5FDstdio.c
index 0168ff4..7056f7f 100644
--- a/src/H5FDstdio.c
+++ b/src/H5FDstdio.c
@@ -24,6 +24,7 @@
* and is not intended for production use!
*/
#include <assert.h>
+#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
@@ -1078,8 +1079,8 @@ H5FD_stdio_truncate(H5FD_t *_file, hid_t /*UNUSED*/ dxpl_id,
* Function: H5FD_stdio_lock
*
* Purpose: Lock a file via flock
- *
* NOTE: This function is a no-op if flock() is not present.
+ *
* Errors:
* IO FCNTL flock failed.
*
@@ -1093,21 +1094,27 @@ static herr_t
H5FD_stdio_lock(H5FD_t *_file, hbool_t rw)
{
#ifdef H5_HAVE_FLOCK
- H5FD_stdio_t *file = (H5FD_stdio_t*)_file;
- int lock; /* The type of lock */
- static const char *func = "H5FD_stdio_lock"; /* Function Name for error reporting */
+ H5FD_stdio_t *file = (H5FD_stdio_t*)_file; /* VFD file struct */
+ int lock_flags; /* file locking flags */
+ static const char *func = "H5FD_stdio_lock"; /* Function Name for error reporting */
/* Clear the error stack */
H5Eclear2(H5E_DEFAULT);
assert(file);
- /* Determine the type of lock */
- lock = rw ? LOCK_EX : LOCK_SH;
+ /* Set exclusive or shared lock based on rw status */
+ lock_flags = rw ? LOCK_EX : LOCK_SH;
- /* Place the lock with non-blocking */
- if(flock(file->fd, lock | LOCK_NB) < 0)
- H5Epush_ret(func, H5E_ERR_CLS, H5E_IO, H5E_FCNTL, "flock failed", -1)
+ /* Place a non-blocking lock on the file */
+ if(flock(file->fd, lock_flags | LOCK_NB) < 0) {
+ if(ENOSYS == errno)
+ H5Epush_ret(func, H5E_ERR_CLS, H5E_IO, H5E_FCNTL, "file locking disabled on this file system (use HDF5_USE_FILE_LOCKING environment variable to override)", -1)
+ else
+ H5Epush_ret(func, H5E_ERR_CLS, H5E_IO, H5E_FCNTL, "file lock failed", -1)
+ } /* end if */
+
+ /* Flush the stream */
if(fflush(file->fp) < 0)
H5Epush_ret(func, H5E_ERR_CLS, H5E_IO, H5E_WRITEERROR, "fflush failed", -1)
@@ -1117,16 +1124,15 @@ H5FD_stdio_lock(H5FD_t *_file, hbool_t rw)
} /* end H5FD_stdio_lock() */
/*-------------------------------------------------------------------------
- * Function: H5F_stdio_unlock
- *
- * Purpose: Unlock a file via flock
+ * Function: H5F_stdio_unlock
*
+ * Purpose: Unlock a file via flock
+ * NOTE: This function is a no-op if flock() is not present.
*
- * NOTE: This function is a no-op if flock() is not present.
* Errors:
* IO FCNTL flock failed.
*
- * Return: Non-negative on success/Negative on failure
+ * Return: Non-negative on success/Negative on failure
*
* Programmer: Vailin Choi; March 2015
*
@@ -1136,18 +1142,25 @@ static herr_t
H5FD_stdio_unlock(H5FD_t *_file)
{
#ifdef H5_HAVE_FLOCK
- H5FD_stdio_t *file = (H5FD_stdio_t*)_file;
- static const char *func = "H5FD_stdio_unlock"; /* Function Name for error reporting */
+ H5FD_stdio_t *file = (H5FD_stdio_t*)_file; /* VFD file struct */
+ static const char *func = "H5FD_stdio_unlock"; /* Function Name for error reporting */
/* Clear the error stack */
H5Eclear2(H5E_DEFAULT);
assert(file);
+ /* Flush the stream */
if(fflush(file->fp) < 0)
H5Epush_ret(func, H5E_ERR_CLS, H5E_IO, H5E_WRITEERROR, "fflush failed", -1)
- if(flock(file->fd, LOCK_UN) < 0)
- H5Epush_ret(func, H5E_ERR_CLS, H5E_IO, H5E_FCNTL, "flock (unlock) failed", -1)
+
+ /* Place a non-blocking lock on the file */
+ if(flock(file->fd, LOCK_UN) < 0) {
+ if(ENOSYS == errno)
+ H5Epush_ret(func, H5E_ERR_CLS, H5E_IO, H5E_FCNTL, "file locking disabled on this file system (use HDF5_USE_FILE_LOCKING environment variable to override)", -1)
+ else
+ H5Epush_ret(func, H5E_ERR_CLS, H5E_IO, H5E_FCNTL, "file unlock failed", -1)
+ } /* end if */
#endif /* H5_HAVE_FLOCK */
diff --git a/src/H5Fint.c b/src/H5Fint.c
index 2895364..9cf129c 100644
--- a/src/H5Fint.c
+++ b/src/H5Fint.c
@@ -171,6 +171,8 @@ H5F_get_access_plist(H5F_t *f, hbool_t app_ref)
latest_format = TRUE;
if(H5P_set(new_plist, H5F_ACS_LATEST_FORMAT_NAME, &latest_format) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set 'latest format' flag")
+ if(H5P_set(new_plist, H5F_ACS_METADATA_READ_ATTEMPTS_NAME, &(f->shared->read_attempts)) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set 'read attempts ' flag")
if(H5P_set(new_plist, H5F_ACS_OBJECT_FLUSH_CB_NAME, &(f->shared->object_flush)) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set object flush callback")
@@ -998,6 +1000,8 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
H5F_close_degree_t fc_degree; /*file close degree */
hbool_t evict_on_close; /* evict on close value from plist */
H5F_t *ret_value = NULL; /*actual return value */
+ char *lock_env_var = NULL;/*env var pointer */
+ hbool_t use_file_locking; /*read from env var */
FUNC_ENTER_NOAPI(NULL)
@@ -1012,6 +1016,16 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
if(NULL == (drvr = H5FD_get_class(fapl_id)))
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, NULL, "unable to retrieve VFL class")
+ /* Check the environment variable that determines if we care
+ * about file locking. File locking should be used unless explicitly
+ * disabled.
+ */
+ lock_env_var = HDgetenv("HDF5_USE_FILE_LOCKING");
+ if(lock_env_var && !HDstrcmp(lock_env_var, "FALSE"))
+ use_file_locking = FALSE;
+ else
+ use_file_locking = TRUE;
+
/*
* Opening a file is a two step process. First we try to open the
* file in a way which doesn't affect its state (like not truncating
@@ -1024,52 +1038,52 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
* way for us to detect it here anyway).
*/
if(drvr->cmp)
- tent_flags = flags & ~(H5F_ACC_CREAT|H5F_ACC_TRUNC|H5F_ACC_EXCL);
+ tent_flags = flags & ~(H5F_ACC_CREAT|H5F_ACC_TRUNC|H5F_ACC_EXCL);
else
- tent_flags = flags;
+ tent_flags = flags;
if(NULL == (lf = H5FD_open(name, tent_flags, fapl_id, HADDR_UNDEF))) {
- if(tent_flags == flags) {
+ if(tent_flags == flags) {
#ifndef H5_USING_MEMCHECKER
time_t mytime = HDtime(NULL);
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: time = %s, name = '%s', tent_flags = %x", HDctime(&mytime), name, tent_flags)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: time = %s, name = '%s', tent_flags = %x", HDctime(&mytime), name, tent_flags)
#else /* H5_USING_MEMCHECKER */
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: name = '%s', tent_flags = %x", name, tent_flags)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: name = '%s', tent_flags = %x", name, tent_flags)
#endif /* H5_USING_MEMCHECKER */
} /* end if */
H5E_clear_stack(NULL);
- tent_flags = flags;
- if(NULL == (lf = H5FD_open(name, tent_flags, fapl_id, HADDR_UNDEF))) {
+ tent_flags = flags;
+ if(NULL == (lf = H5FD_open(name, tent_flags, fapl_id, HADDR_UNDEF))) {
#ifndef H5_USING_MEMCHECKER
time_t mytime = HDtime(NULL);
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: time = %s, name = '%s', tent_flags = %x", HDctime(&mytime), name, tent_flags)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: time = %s, name = '%s', tent_flags = %x", HDctime(&mytime), name, tent_flags)
#else /* H5_USING_MEMCHECKER */
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: name = '%s', tent_flags = %x", name, tent_flags)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: name = '%s', tent_flags = %x", name, tent_flags)
#endif /* H5_USING_MEMCHECKER */
} /* end if */
} /* end if */
/* Is the file already open? */
if((shared = H5F_sfile_search(lf)) != NULL) {
- /*
- * The file is already open, so use that one instead of the one we
- * just opened. We only one one H5FD_t* per file so one doesn't
- * confuse the other. But fail if this request was to truncate the
- * file (since we can't do that while the file is open), or if the
- * request was to create a non-existent file (since the file already
- * exists), or if the new request adds write access (since the
- * readers don't expect the file to change under them).
- */
- if(H5FD_close(lf) < 0)
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to close low-level file info")
- if(flags & H5F_ACC_TRUNC)
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to truncate a file which is already open")
- if(flags & H5F_ACC_EXCL)
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "file exists")
- if((flags & H5F_ACC_RDWR) && 0 == (shared->flags & H5F_ACC_RDWR))
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "file is already open for read-only")
+ /*
+ * The file is already open, so use that one instead of the one we
+ * just opened. We only one one H5FD_t* per file so one doesn't
+ * confuse the other. But fail if this request was to truncate the
+ * file (since we can't do that while the file is open), or if the
+ * request was to create a non-existent file (since the file already
+ * exists), or if the new request adds write access (since the
+ * readers don't expect the file to change under them).
+ */
+ if(H5FD_close(lf) < 0)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to close low-level file info")
+ if(flags & H5F_ACC_TRUNC)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to truncate a file which is already open")
+ if(flags & H5F_ACC_EXCL)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "file exists")
+ if((flags & H5F_ACC_RDWR) && 0 == (shared->flags & H5F_ACC_RDWR))
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "file is already open for read-only")
/* Allocate new "high-level" file struct */
if((file = H5F_new(shared, flags, fcpl_id, fapl_id, NULL)) == NULL)
@@ -1089,8 +1103,19 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
if(NULL == (lf = H5FD_open(name, flags, fapl_id, HADDR_UNDEF)))
HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file")
} /* end if */
+
+ /* Place an advisory lock on the file */
+ if(use_file_locking)
+ if(H5FD_lock(lf, (hbool_t)((flags & H5F_ACC_RDWR) ? TRUE : FALSE)) < 0) {
+ /* Locking failed - Closing will remove the lock */
+ if(H5FD_close(lf) < 0)
+ HDONE_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to close low-level file info")
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to lock the file")
+ } /* end if */
+
+ /* Create the 'top' file structure */
if(NULL == (file = H5F_new(NULL, flags, fcpl_id, fapl_id, lf)))
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to create new file object")
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to initialize file structure")
} /* end else */
/* Retain the name the file was opened with */
@@ -1121,15 +1146,16 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
*/
if(H5G_mkroot(file, dxpl_id, TRUE) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, NULL, "unable to create/open root group")
- } else if (1 == shared->nrefs) {
+ } /* end if */
+ else if (1 == shared->nrefs) {
- /* Read the superblock if it hasn't been read before. */
+ /* Read the superblock if it hasn't been read before. */
if(H5F__super_read(file, dxpl_id, TRUE) < 0)
- HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock")
+ HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock")
- /* Open the root group */
- if(H5G_mkroot(file, dxpl_id, FALSE) < 0)
- HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to read root group")
+ /* Open the root group */
+ if(H5G_mkroot(file, dxpl_id, FALSE) < 0)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to read root group")
} /* end if */
/* Get the file access property list, for future queries */
@@ -1150,7 +1176,8 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
shared->fc_degree = lf->cls->fc_degree;
else
shared->fc_degree = fc_degree;
- } else if(shared->nrefs > 1) {
+ } /* end if */
+ else if(shared->nrefs > 1) {
if(fc_degree == H5F_CLOSE_DEFAULT && shared->fc_degree != lf->cls->fc_degree)
HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, NULL, "file close degree doesn't match")
if(fc_degree != H5F_CLOSE_DEFAULT && fc_degree != shared->fc_degree)
@@ -1174,19 +1201,19 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
/* Formulate the absolute path for later search of target file for external links */
if(H5_build_extpath(name, &file->extpath) < 0)
- HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, NULL, "unable to build extpath")
+ HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, NULL, "unable to build extpath")
/* Formulate the actual file name, after following symlinks, etc. */
if(H5F_build_actual_name(file, a_plist, name, &file->actual_name) < 0)
- HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, NULL, "unable to build actual name")
+ HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, NULL, "unable to build actual name")
/* Success */
ret_value = file;
done:
if(!ret_value && file)
- if(H5F_dest(file, dxpl_id, FALSE) < 0)
- HDONE_ERROR(H5E_FILE, H5E_CANTCLOSEFILE, NULL, "problems closing file")
+ if(H5F_dest(file, dxpl_id, FALSE) < 0)
+ HDONE_ERROR(H5E_FILE, H5E_CANTCLOSEFILE, NULL, "problems closing file")
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_open() */
diff --git a/src/H5Zscaleoffset.c b/src/H5Zscaleoffset.c
index 91a6c00..1cca9b1 100644
--- a/src/H5Zscaleoffset.c
+++ b/src/H5Zscaleoffset.c
@@ -667,58 +667,6 @@ H5Z_class2_t H5Z_SCALEOFFSET[1] = {{
H5Z_scaleoffset_modify_4(i, type, pow_fun, buf, d_nelmts, min, D_val) \
}
-/* Include our own rounding routine and alias it to the stdc macros, if they
- * aren't available.
- */
-#if !(defined(H5_HAVE_LLROUND) && defined(H5_HAVE_LLROUNDF) && defined(H5_HAVE_LROUND) && defined(H5_HAVE_LROUNDF) && defined(H5_HAVE_ROUND) && defined(H5_HAVE_ROUNDF))
-/* Round a floating-point value to the nearest integer value 4/19/05 */
-/* rounding to the bigger absolute value if val is in the middle,
- 0.5 -> 1, -0.5 ->-1
-5/9/05, KY */
-static double
-H5Z__scaleoffset_rnd(double val)
-{
- double u_val, l_val;
-
- u_val = HDceil(val);
- l_val = HDfloor(val);
-
- if(val > 0) {
- if((u_val - val) <= (val - l_val))
- return u_val;
- else
- return l_val;
- } /* end if */
- else {
- if((val - l_val) <= (u_val - val))
- return l_val;
- else
- return u_val;
- }
-} /* H5Z__scaleoffset_rnd() */
-
-/* Alias rounding macros to routine above, if not defined */
-#if !defined(H5_HAVE_LLROUND)
-#define llround(x) H5Z__scaleoffset_rnd(x)
-#endif /* !defined(H5_HAVE_LLROUND) */
-#if !defined(H5_HAVE_LLROUNDF)
-#define llroundf(x) H5Z__scaleoffset_rnd(x)
-#endif /* !defined(H5_HAVE_LLROUNDF) */
-#if !defined(H5_HAVE_LROUND)
-#define lround(x) H5Z__scaleoffset_rnd(x)
-#endif /* !defined(H5_HAVE_LROUND) */
-#if !defined(H5_HAVE_LROUNDF)
-#define lroundf(x) H5Z__scaleoffset_rnd(x)
-#endif /* !defined(H5_HAVE_LROUNDF) */
-#if !defined(H5_HAVE_ROUND)
-#define round(x) H5Z__scaleoffset_rnd(x)
-#endif /* !defined(H5_HAVE_ROUND) */
-#if !defined(H5_HAVE_ROUNDF)
-#define roundf(x) H5Z__scaleoffset_rnd(x)
-#endif /* !defined(H5_HAVE_ROUNDF) */
-
-#endif /* !(defined(H5_HAVE_LLROUND) && defined(H5_HAVE_LLROUNDF) && defined(H5_HAVE_LROUND) && defined(H5_HAVE_LROUNDF) && defined(H5_HAVE_ROUND) && defined(H5_HAVE_ROUNDF)) */
-
/*-------------------------------------------------------------------------
* Function: H5Z_can_apply_scaleoffset